His presidency was marked by attempts to revive the Ecuadorian economy, which was in a recession at the time, including the freeing of $400 million US dollars worth of assets frozen by the previous government. He left office in 2003 after Lucio Gutiérrez was victorious in the 2002 presidential election.

After his term ended, accusations of irregularities in foreign debt negotiation that cost the country $9 billion dollars were levelled at the former president. He completely denied the charges, which could have had him sent to jail for twenty five years if convicted. Claiming that he was the victim of unfair persecution, he applied for political asylum in the Dominican Republic, which was granted on August 11, 2003. The Supreme Court case against him was annulled by an unconstitutional, yet functioning, Supreme Court on grounds that the case was not initiated by a two-thirds congressional vote as the Constitution stipulates. Shortly after, however, the presidency of Lucio Gutiérrez ended and the charges were reinstated. He was placed under house arrest in May 2005 and Ecuador's Interior Minister planned to prosecute. On March 16, 2006, a Supreme Court judge lifted the detention order, and charged Noboa of being an accessory after the fact. Noboa said he would appeal this charge as well.[1]